A Missouri judge recently granted parental rights to a couple who wants to adopt a little boy — despite the objections of the boy’s undocumented mother. The Guatemalan mother had been jailed following an immigration raid, but judges ruled she had abandoned her child. The case, which generated national and international headlines, has raised concerns and questions from child and immigration advocates about the fate of thousands of U.S.-born children whose parents have been arrested and/or deported.

In the Missouri case, a pregnant Guatemalan woman, Encarnacion Bail Romero, entered the country illegally and used a false social security number to gain employment. She later gave birth in Missouri to a baby boy. In 2007, while working at a poultry plant, she was arrested in an immigration raid and jailed. Separated from her child, relatives were forced to take care of her baby boy, Carlos. Friends of the relatives later took over caring for the boy. According to reports, those friends found a couple, Melinda and Seth Moser, who wanted a baby, and they let the Mosers take care of Carlos. The Mosers began to calling Carlos by a new name — Jamison. This was only 5 months after Carlos’ mother was arrested, and the Mosers quickly filed for adoption, arguing that Bail Romero had abandoned her child.

Bail Romero’s attorney, as well as child and immigration advocates, say this is not a case of abandonment. They say the undocumented mother was held in a jail without legal representation initially and given information she did not understand; she does not speak English. In fact, her first language is not Spanish but an Indian dialect. When she finally received paperwork as well as information that the couple wanted to adopt her baby boy, she refused to sign the papers, saying she only wanted her boy to be cared for until she got out. But a family court judge agreed with the Mosers that Bail Romero had “abandoned” her child, and granted parental rights to the Mosers.

When Bail Encarnacion was released in 2009, she fought to regain custody. The State Supreme Court agreed with Encarnacion and ruled that state adoption laws had not been followed properly by the previous judge. The latest ruling, however, does find the undocumented mother abandoned her child, and grants parental rights to the Mosers, who have been virtually the only parents the boy knows. He is almost six, and the ruling clears the path for the Mosers to adopt him.

“While the particulars of this case might be unusual, we are seeing an increasing number of instances where the parental rights of undocumented immigrants are being terminated,” says Wendy Cervantes, vice president for immigration and child rights policy at First Focus. Cervantes worries the case will set a precedent where more judges will determine it is not in the best interest of a child to be returned to a mother or father who might be deported. There are 5.5 million children in this country who currently live with at least one undocumented parent.

According to Department of Homeland statistics, 46,486 parents of U.S.-citizen children were removed from the country during the first six months of 2011. This is half of the total number of adults deported between 1997 and 2007; in those ten years, 108,000 undocumented parents were deported.

“My biggest concern is what is happening to the children of the more than 46,000 parents who were removed from this country,” says Cervantes. Part of the problem, say advocates like Cervantes, is that there is no uniform policy for immigration enforcement activity. “We are working with ICE to allow a parent a phone call when they are apprehended,” she says. Though there are guidelines for raids involving more than 25 people, what happens to the children of undocumented parents depends on local coordination between child welfare agencies and local law enforcement, as well as ICE.

There were more than 5,000 children of undocumented parents in foster care in 22 states, and 15,000 more are expected to join the foster rolls, according to figures from the Applied Research Center.

California Congresswoman Lucille Roybal-Allard recently introduced a bill, HR6128, the Help Separated Families Act, to ensure that immigration status alone does not terminate a parent’s parental rights. “People, regardless of their immigration status, deserve to know that their children are cared for,” said Congresswoman Roybal-Allard in a previous statement.

The bill was supported by more than 100 religious, civic, immigrants rights, women’s, Latino and Asian American groups. This builds on the Help For Separated Children Act which had been introduced by Minnesota Senator Al Franken. The bill provides for nationwide protocols and guidelines such as allowing apprehended parents to make phone calls to arrange for the care of their children, as well as information on legal service providers for parents. Just as importantly, the bill calls for improved coordination between ICE, child welfare agencies, and non-profits that help immigrant families.

“The current policies do not make sense,” says Cervantes. “It’s an economic strain for everyone involved, the children are emotionally sad and traumatized, and they are hurting these U.S. citizens all over the country.”